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A number of studies have demonstrated that patients with autoimmune disease have lower levels of vitamin D prompting speculation that vitamin D might suppress inflammation and immune responses in children with juvenile idiopathic arthritis (JIA). The objective of this study was to compare vitamin D levels in children with JIA at disease onset with healthy children. We hypothesized that children and adolescents with JIA have lower vitamin D levels than healthy children and adolescents. Data from a Canadian cohort of children with new-onset JIA (n= 164, data collection 2007-2012) were compared to Canadian Health Measures Survey (CHMS) data (n=4027, data collection 2007-2011). We compared 25-hydroxy vitamin D (25(OH)D) concentrations with measures of inflammation, vitamin D supplement use, milk intake, and season of birth. Mean 25(OH)D level was significantly higher in patients with JIA (79 ± 3.1 nmol/L) than in healthy controls (68 ± 1.8 nmol/L P.05). Patients with JIA more often used vitamin D containing supplements (50% vs. 7%; P.05). The prevalence of 25(OH)D deficiency (30 nmol/L) was 6% for both groups. Children with JIA with 25(OH)D deficiency or insufficiency (50 nmol/L) had higher C-reactive protein levels. Children with JIA were more often born in the fall and winter compared to healthy children. In contrast to earlier studies, we found vitamin D levels in Canadian children with JIA were higher compared to healthy children and associated with more frequent use of vitamin D supplements. Among children with JIA, low vitamin D levels were associated with indicators of greater inflammation.

Individual variability in responses to vaccination can result in vaccinated subjects failing to develop a protective immune response. Vaccine non-responders can remain susceptible to infection and may compromise efforts to achieve herd immunity. Biomarkers of vaccine unresponsiveness could aid vaccine research and development as well as strategically improve vaccine administration programs. We previously vaccinated piglets (n = 117) against a commercial Mycoplasma hyopneumoniae vaccine (RespiSure-One) and observed in low vaccine responder piglets, as defined by serum IgG antibody titers, differential phosphorylation of peptides involved in pro-inflammatory cytokine signaling within peripheral blood mononuclear cells (PBMCs) prior to vaccination, elevated plasma interferon-gamma concentrations, and lower birth weight compared to high vaccine responder piglets. In the current study, we use kinome analysis to investigate signaling events within PBMCs collected from the same high and low vaccine responders at 2 and 6 days post-vaccination. Furthermore, we evaluate the use of inflammatory plasma cytokines, birthweight, and signaling events as biomarkers of vaccine unresponsiveness in a validation cohort of high and low vaccine responders. Differential phosphorylation events (FDR 0.05) within PBMCs are established between high and low responders at the time of vaccination and at six days post-vaccination. A subset of these phosphorylation events were determined to be consistently differentially phosphorylated (p 0.05) in the validation cohort of high and low vaccine responders. In contrast, there were no differences in birth weight (p 0.5) and plasma IFNγ concentrations at the time of vaccination (p 0.6) between high and low responders within the validation cohort. The results in this study suggest, at least within this study population, phosphorylation biomarkers are more robust predictors of vaccine responsiveness than other physiological markers.

Alignment of protein sequences is fundamental in analyzing homology, evolutionary events and functional relationships. Searching for the epitopic peptide platform underlying hepatitis C virus (HCV) infection and autoimmune phenomena, we have used sequence-sequence peptide matching to compare the HCV polyprotein sequence to the human proteome. The following results were obtained: (1) pentamers from HCV polyprotein have a widespread and high level of similarity to a large number of human proteins (19,605 human proteins, that is 57.6% of the human proteome); (2) remarkable similarity between the two proteomes persists even using longer peptide motifs as probes for identity scanning; (3) only a limited number of HCV pentameric fragments have no similarity to the human host, so representing molecular sequence signatures of the virus. We conclude that the widespread sharing of numerous perfect exact matches between HCV and human proteomes might explain HCV persistence in humans.

A machine vision system was used to classify pistachio nuts into four grades designated as “Grade 1”, “Grade 2”, “Grade 3” and “unsplit”, respectively. Fourier descriptors and the projected area (pixel count) of the individual nuts were extracted from their two-dimensional images and used as recognition features. The Fisher criterion for feature selection was used in conjunction with the Gaussian classification method to select a subset of the Fourier descriptors from an initial set of 15 harmonics. The results of this feature selection indicated that seven harmonics were sufficient for this classification problem. The selected Fourier descriptors and the area of each nut were subsequently used as inputs to two classification schemes: a hybrid decision-tree classifier and a feedforward neural network trained by back-propagation. The average classification accuracy obtained for the decision-tree classifier was 87·1%. The neural-network classifier resulted in an average classification accuracy of 94·8%, indicating the superiority of the neural-network approach for machine vision grading of these nuts.

This paper presents a declarative approach to secondary storage in a logic programming environment. We begin with a simple, but powerful, storage model which unifies the ideas of nonvolatile storage and a file system. Using a parallel logic programming language, a succinct specification of the model is given. The specification, with minor modification, forms an implementation. The implementation is described and critiqued. An improved second model is presented which advocates secondary storage through a declarative nonvolatile storage medium and a separate file system. An implementation is again easily realized. Features of the implementation are discussed. This work develops a model and implementation of term-based, declarative I/O. Side effects and destructive assignment are avoided. Concepts developed include device processors, unique compact representations, and lazy-term expansion. Information transfer is unification based, so file abstractions do not require explicit read and write operations. The parallel logic program language used is Concurrent Prolog.